2024

S. Mukherjee, B. Babadi, and S. A. Shamma, Sparse high-dimensional decomposition of non-primary auditory cortical receptive fields, to appear in PLOS Computational Biology, 2024.

L. C. Parra, A. Silvan, M. Nentwich, J. Madsen, V. E. Parra, and B. Babadi, VARX Granger analysis: Models for neuroscience, physiology, sociology and econometrics, to appear in PLOS ONE, 2024.

S. Mukherjee and B. Babadi, Adaptive modeling and inference of higher-order coordination in neuronal assemblies: a dynamic greedy estimation approach, PLoS Computational Biology, Vol. 20, No. 5, e1011605, 2024.

K. Pathirage†, A. Virmani†, A. J. Scott, R. J. Traub, R. K. Ernst, R. Ghodssi, B. Babadi, and P. A. Abshire, Interpretable dimensionality reduction and classification of mass spectrometry imaging data in a visceral pain model via non-negative matrix factorization, PLoS ONE, Vol. 19, No. 10, e0300526, 2024 († denotes co-first authorship).

B. Soleimani, I.M. D. Karunathilake, P. Das, S. E. Kuchinsky, B. Babadi, and J. Z. Simon, Changes in Cortical Directional Connectivity during Difficult Listening in Younger and Older Adults, preprint, 2023.

S. P. Hajiseyedrazi and B. Babadi, An Instrumental Variable Approach to Functional Network Discovery from Optogenetic Experiments, to appear in the Proceedings of the 58th Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, Oct. 27 – 30, 2024.

R. Abeyesekara, J. Z. Simon, and B. Babadi, Variational Covariance Smoothing for Dynamic Functional Connectivity Analysis, to appear in the Proceedings of the 58th Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, Oct. 27 – 30, 2024.

M. Nentwich, B. Babadi, S. Bickel, and L. C. Parra, VARX model of the Brain: Functional connectivity dominates response to natural stimulus in human intracranial EEG, Proceedings of the 2024 Annual Conference on Cognitive Computational Neuroscience, Boston, MA, Aug. 6-9, 2024.

S. Mukherjee, P. Jendrichovsky, P. O. Kanold, and B. Babadi, Reinforcement Learning-guided Optogenetic Stimulation Policies For Robust Functional Network Discovery, Proceedings of the 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2024), Seoul, Korea, April 14-19, 2024.

2023

K. M. O’Neill, E. D. Anderson‡, S. Mukherjee‡, S. Gandu‡, S. A. McEwan, A. Omelchenko, A. R. Rodriguez, W. Losert, D. F. Meaney, B. Babadi, and B. L. Firestein, Time-dependent homeostatic mechanisms underlie Brain-Derived Neurotrophic Factor action on neural circuitry, Communications Biology, Vol. 6, Article No. 1278, 2023 (‡ denotes co-second authorship).

L. Koçillari, M. Celotto, N. A. Francis, S. Mukherjee, B. Babadi, P. O. Kanold, and S. Panzeri, Behavioural relevance of redundant and synergistic stimulus information between functionally connected neurons in mouse auditory cortex, Brain Informatics, Vol. 10, Article No. 34, 2023.

P. Das and B. Babadi, Non-Asymptotic Guarantees for Reliable Identification of Granger Causality via the LASSO, IEEE Transactions on Information Theory, Vol. 69, No. 11, pp. 7439–7460, 2023.

B. Soleimani, I. Dallasta, P. Das, J. P. Kulasingham, S. Girgenti, J. Z. Simon, B. Babadi, and E. B. Marsh, Altered Directional Functional Connectivity Underlies Post-Stroke Cognitive Recovery, Brain Communications, Vol. 5, No. 3, fcad149, 2023.

R. Abeysekara, C. J. Smalt, I.M. D. Karunathilake, J. Z. Simon, and B. Babadi, Information-Theoretic Limits on the Performance of Auditory Attention Decoders, to appear in the Proceedings of the 57th Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, Oct. 29 – Nov. 1, 2023.

L. Kocçillari, M. Celotto, N. A. Francis, S. Mukherjee, B. Babadi, P. O. Kanold, and S. Panzeri, Measuring stimulus-related redundant and synergistic functional connectivity with single cell resolution in auditory cortex, Proceedings of the 16th International Conference on Brain Informatics (BI 2023), August 1-3, 2023, Hoboken & New York, USA.

B. Soleimani, I.M. D. Karunathilake, P. Das, S. E. Kuchinsky, B. Babadi, and J. Z. Simon, Changes in Cortical Directional Connectivity during Difficult Speech Listening in Younger and Older Adults, Proceedings of the 52nd Annual Neuroscience Meeting (SfN 2023), Nov. 11—15, 2023.

2022

B. Soleimani, P. Das, I.M. D. Karunathilake, S. E. Kuchinsky, J. Z. Simon, and B. Babadi, NLGC: Network Localized Granger Causality with Application to MEG Directional Functional Connectivity Analysis, NeuroImage, Vol. 260, 119496, 2022 [Code].

N. A. Francis, S. Mukherjee, L. Koçillari, S. Panzeri, B. Babadi, and P. O. Kanold, Sequential Transmission of Task-Relevant Information in Cortical Neuronal Networks, Cell Reports, Vol. 39, No. 9, 110878, May 2022.

S. Khosravi, A. Rupasinghe, and B. Babadi, Granger Causal Inference from Spiking Observations via Latent Variable Modeling, Proceedings of the 2022 Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, Oct. 30 – Nov. 2, 2022.

S. Khosravi, A. Rupasinghe, and B. Babadi, Inferring Directional Connectivity from Spiking Observations via Latent Variable Modeling, Proceedings of the 51st Annual Neuroscience Meeting (SfN 2022), Nov. 11—15, 2022.

B. Soleimani, I. M. D. Karunathilake, P. Das, S. E. Kuchinsky, J. Z. Simon, and B. Babadi, Assessing Directional Connectivity via Network Localized Granger Causality Extracted from MEG Data, Proceedings of the 51st Annual Neuroscience Meeting (SfN 2022), Nov. 11—15, 2022.

2021

A. Rupasinghe, N. Francis, J. Liu, Z. Bowen, P. O. Kanold, and B. Babadi, Direct Extraction of Signal and Noise Correlations from Two-Photon Calcium Imaging of Ensemble Neuronal Activity, eLife, 10:e68046, 2021 [Data] [Code].

S. Mukherjee and B. Babadi, Dynamic Analysis of Higher-Order Coordination in Neuronal Assemblies via De-Sparsified Orthogonal Matching Pursuit, 2021 Neural Information Processing Systems (NeurIPS 2021), Dec. 6-14, 2021.

B. Babadi, Neural Encoding and Decoding, Book Chapter in the Handbook of Neuroengineering, Ed. Nitish V. Thakor, Springer, 2021.

B. Soleimani, I. M. D. Karunathilake, P. Das, S. E. Kuchinsky, B. Babadi, and J. Z. Simon, Network localized Granger causality reveals cortical network changes under difficult listening conditions, Proceedings of the 50th Annual Neuroscience Meeting (SfN 2021), Nov. 8—11, 2021.

S. Mukherjee, B. Babadi, and S. A. Shamma, Sparse high-dimensional decomposition of non-primary cortical spectrotemporal receptive fields, Proceedings of the 50th Annual Neuroscience Meeting (SfN 2021), Nov. 8—11, 2021.

A. Rupasinghe, N. Francis, J. Liu, Z. Bowen, P. O. Kanold, and B. Babadi, Direct inference of signal and noise correlations from two-photon calcium imaging data without intermediate spike deconvolution, Proceedings of the 50th Annual Neuroscience Meeting (SfN 2021), Nov. 8—11, 2021.

2020

S. Miran, A. Presacco, J. Z. Simon, M. C. Fu, S. I. Marcus, and B. Babadi, Dynamic Estimation of Auditory Temporal Response Functions via State-Space Models with Gaussian Mixture Process Noise, PLoS Computational Biology, Vol. 16, No. 8, e1008172, 2020 [Code].

A. Rupasinghe and B. Babadi, Multitaper Analysis of Semi-Stationary Spectra from Multivariate Neuronal Spiking Observations, IEEE Trans. on Signal Processing, Vol. 68, pp. 4382–4396, 2020 [Code].

P. Das, C. Brodbeck, J. Z. Simon, and B. Babadi, Neuro-Current Response Functions: A Unified Approach to MEG Source Analysis under the Continuous Stimuli Paradigm, NeuroImage, Vol. 211, 116528, May 2020 [Supplementary Videos: 1, 2, 3] [Code].

P. Das and B. Babadi, Multitaper Spectral Analysis of Neuronal Spiking Activity Driven by Latent Stationary Processes, Signal Processing, Vol. 170, 107429, May 2020 [Code].

A. Rupasinghe, S. Mukherjee, and B. Babadi, Adaptive Frequency-domain Granger Causal Inference from Neuronal Ensemble Data, Proceedings of the 54th Asilomar Conference on Signals, Systems, and Computers, Nov. 1-4, Pacific Grove, CA.

A. Rupasinghe and B. Babadi, Robust Inference of Neuronal Correlations from Blurred and Noisy Spiking Observations, Proceedings of the 54th Conference on Information Sciences and Systems (CISS 2020), March 18-20, Princeton, NJ.

B. Soleimani, P. Das, J. Kulasingham, J. Z. Simon, and B. Babadi, Granger Causal Inference from Indirect Low-Dimensional Measurements with Application to MEG Functional Connectivity Analysis, Proceedings of the 54th Conference on Information Sciences and Systems (CISS 2020), March 18-20, Princeton, NJ.

B. Babadi, Learning from a Neuroscience Perspective, Book Chapter in Computer Vision: A Reference Guide (Living Edition), Ed. Katsushi Ikeuchi, Springer International Publishing AG, 2020.

2019

J. Liu, M. R. Whiteway, A. Sheikhattar, D. A. Butts, B. Babadi, and P. O. Kanold, Parallel Processing of Sound Dynamics across Mouse Auditory Cortex via Spatially Patterned Thalamic Inputs and Distinct Areal Intracortical Circuits, Cell Reports, Vol. 27, No. 3, pp. 872–885.E7, April 16, 2019.

S. Mukherjee and B. Babadi, A Statistical Approach to Dynamic Synchrony Analysis of Neuronal Ensemble Spiking, Proceedings of the 2019 Asilomar Conference on Signals, Systems, and Computers, Nov. 3-6, Pacific Grove, CA.

A. Presacco, S. Miran, B. Babadi, and J. Z. Simon, Real-Time Tracking of Magnetoencephalographic Neuromarkers during a Dynamic Attention-Switching Task, Proceedings of the 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC’2019), July 23–27, Berlin, Germany.

A. Rupasinghe and B. Babadi, Multitaper Analysis of Evolutionary Spectral Density Matrix from Multivariate Spiking Observations, Proceedings of the 2019 IEEE Data Science Workshop, June 2–5, Minneapolis, MN.

S. Miran, J. Z. Simon, M. C. Fu, S. I. Marcus, and B. Babadi, Estimation of State-Space Models with Gaussian Mixture Process Noise, Proceedings of the 2019 IEEE Data Science Workshop, June 2–5, Minneapolis, MN.

S. Mukherjee, K. M. O’Neill, B. L. Firestein, W. Losert, and B. Babadi, A Statistical Approach to the Dynamic Analysis of Synchronous Spiking in Neuronal Ensembles, Proceedings of the 49th Annual Neuroscience Meeting (SfN 2019), Oct. 19—23, Chicago, IL.

2018

E. Pirondini, B. Babadi, G. Obregon-Henao, C. Lamus, W. Q. Malik, M. S. Hämäläinen, and P. L. Purdon, Computationally-efficient Algorithms for Sparse, Dynamic Solutions to the EEG Source Localization Problem, IEEE Trans. on Biomedical Engineering, Vol. 65, Np. 6, June 2018.

S. Miran, S. Akram, A. Sheikhattar, J. Z. Simon, T. Zhang, and B. Babadi, Real-Time Tracking of Selective Auditory Attention from M/EEG: A Bayesian Filtering Approach, Frontiers in Neuroscience, Vol. 12, pp. 262, May 2018 [Code].

A. Sheikhattar, S. Miran, J. Liu, J. B. Fritz, S. A. Shamma, P. O. Kanold, and B. Babadi, Extracting Neuronal Functional Network Dynamics via Adaptive Granger Causality Analysis, Proceedings of the National Academy of Sciences, Vol. 115, No. 17, E3869-E3878, April 2018 [Data] [Code].

P. Das and B. Babadi, Dynamic Bayesian Multitaper Spectral Analysis, IEEE Trans. on Signal Processing, Vol. 66, No. 6, pp. 1394-1409, March 2018 [Code].

N. A. Francis, D. E. Winkowski, A. Sheikhattar, K. Armengol, B. Babadi, and P. O. Kanold, Small Networks Encode Decision-Making in Primary Auditory Cortex, Neuron, Vol. 97, No. 4, Feb. 21, 2018.

P. Krishnaswamy, G. Obregon-Henao, J. Ahveninen, S. Khan, B. Babadi, J. Eugenio Iglesias, M. S. Hämäläinen, and P. L. Purdon, Sparsity Enables Estimation of both Subcortical and Cortical Activity from MEG and EEG, Proceedings on the National Academy of Sciences, Vol. 114, No. 48, E10465-E10474, Jan. 2018.

A. Kazemipour, J. Liu, K. Solarana, D. A. Nagode, P. O. Kanold, M. Wu, and B. Babadi, Fast and Stable Signal Deconvolution via Compressible State-Space Models, IEEE Trans. on Biomedical Engineering, Vol. 65, No. 1, pp. 74-86, Jan. 2018 [Code].

P. Das, C. Brodbeck, J. Z. Simon, and B. Babadi, Cortical Localization of the Auditory Temporal Response Function from MEG via Non-convex Optimization, 2018 Asilomar Conference on Signals, Systems, and Computers, Oct. 28-31, Pacific Grove, CA.

S. Miran, S. Akram, A. Sheikhattar, J. Z. Simon, T. Zhang, and B. Babadi, Real-Time Decoding of Auditory Attention from EEG via Bayesian Filtering, Proceedings of the 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC’2018), July 17–21, Honolulu, HI.

B. Babadi, Sparsity Meets Dynamics: Robust Solutions to Neuronal Identification and Inverse Problems, Book Chapter in Dynamic Neuroscience, Eds. Z. Chen and S. Sarma, Springer International Publishing AG, 2018.

2017

S. Miran, P. L. Purdon, E. N. Brown, and B. Babadi, Robust Estimation of Sparse Narrowband Spectra from Neuronal Spiking Data, IEEE Trans. on Biomedical Engineering, Vol. 64, No. 10, pp. 2462-2474, Oct. 2017 [Code].

S. Akram, J. Z. Simon, and B. Babadi, Dynamic Estimation of the Auditory Temporal Response Function from MEG in Competing-Speaker Environments, IEEE Trans. on Biomedical Engineering, Vol. 64, No. 8, pp. 1896-1905, Aug. 2017 [Code].

A. Kazemipour, M. Wu, and B. Babadi, Robust Estimation of Self-Exciting Generalized Linear Models with Application to Neuronal Modeling, IEEE Trans. on Signal Processing, Vol. 65, No. 14, pp. 3733-3748, July 2017 [Code].

A. Kazemipour, S. Miran, P. Pal, B. Babadi, and M. Wu, Sampling Requirements for Stable Autoregressive Estimation, IEEE Trans. on Signal Processing, Vol. 65, No. 9, pp. 2333-2347, May 2017.

C.-C. Chou, C. Gadisetti, T. Shin, N. Devasahayam, A. McMillan, B. Babadi, R. Gullapalli, M. Cherukuri, and J. Zhuo, Accelerated Electron Paramagnetic Resonance Imaging Using Partial Fourier Compressed Sensing Reconstruction, Magnetic Resonance Imaging, Vol. 37, pp. 90-99, April 2017.

P. Das and B. Babadi, A Bayesian Multitaper Method for Nonstationary Data with Application to EEG Analysis, 2017 IEEE Signal Processing in Medicine and Biology Symposium (SPMB17), Dec. 2, Philadelphia, PA.

A. Sheikhattar, S. K. Sorooshyari, B. Babadi, An Autoregressive Approach to Inference in Populations of Correlated Stochastic Neurons, 2017 Asilomar Conference on Signals, Systems, and Computers, Oct. 29–Nov. 1, Pacific Grove, CA.

A. Kazemipour, B. Babadi, M. Wu, K. Podgorski, S. Druckmann, Multiplicative Updates for Optimization Problems with Dynamics, 2017 Asilomar Conference on Signals, Systems, and Computers, Oct. 29–Nov. 1, Pacific Grove, CA.

S. Miran, P. L. Purdon, E. N. Brown, and B. Babadi, Sparse Spectral Estimation from Point Process Observations, Proceedings of the 42nd IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP2017), March 5–9, New Orleans, LA.

S. Miran, S. Akram, J. Z. Simon, T. Zhang, and B. Babadi, Real-time Tracking of the Selective Auditory Attention from M/EEG via Bayesian Filtering, Proceedings of the 47th Annual Neuroscience Meeting (SfN 2017), Nov. 11—15, Washington, DC.

A. Sheikhattar, S. Miran, J. Liu, J. B. Fritz, S. A. Shamma, P. O. Kanold, and B. Babadi, Adaptive Granger Causality Analysis Reveals Functional Network Dynamics Underlying Attentive Behavior at Neuronal Scale, Proceedings of the 47th Annual Neuroscience Meeting (SfN 2017), Nov. 11—15, Washington, DC.

N. A. Francis, D. E. Winkowski, Z. Bowen, A. Sheikhattar, K. Armengol, B. Babadi, D. Plenz, and P. O. Kanold, Neural Correlates of Decision-Making in Primary Auditory Cortex Neuronal Populations, Proceedings of the 47th Annual Neuroscience Meeting (SfN 2017), Nov. 11—15, Washington, DC.

2016

A. Sheikhattar, J. B. Fritz, S. A. Shamma, and B. Babadi, Recursive Sparse Point Process Regression with Application to Spectrotemporal Receptive Field Plasticity Analysis, IEEE Trans. on Signal Processing, Vol. 64, No. 8, pp. 2026—2039, April 2016.

S. Akram, A. Presacco, J. Z. Simon, S. A. Shamma, and B. Babadi, Robust Decoding of Selective Auditory Attention from MEG in a Competing-Speaker Environment via State-Space Modeling, NeuroImage, Vol. 124, Part A, pp. 906—917, Jan. 2016.

A. Kazemipour, J. Liu, P. Kanold, M. Wu, and B. Babadi, Efficient Estimation of Compressible State-Space Models with Application to Calcium Signal Deconvolution, Proceedings of the 2016 IEEE Global Conference on Signal and Information Processing, Dec. 7–9, Washington, DC.

A. Sheikhattar, S. Miran, J. B. Fritz, S. A. Shamma, and B. Babadi, Probing the Functional Circuitry Underlying Auditory Attention via Dynamic Granger Causality Analysis, 2016 Asilomar Conference on Signals, Systems, and Computers, Nov. 6–9, Pacific Grove, CA (invited).

A. Sheikhattar and B. Babadi, Real-time Algorithms for Sparse Neuronal System Identification, Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC’16), Aug. 16–20, Orlando, FL.

A. Sheikhattar and B. Babadi, Dynamic Estimation of Causal Influences in Sparsely-Interacting Neuronal Ensembles, Proceedings of the 50th Annual Conference on Information Sciences and Systems (CISS 2016), March 16–18, Princeton, NJ (invited).

A. Kazemipour, B. Babadi, and M. Wu, Sufficient Conditions for Stable Recovery of Sparse Autoregressive Models, Proceedings of the 50th Annual Conference on Information Sciences and Systems (CISS 2016), March 16–18, Princeton, NJ.

2015

A. Sheikhattar, J. B. Fritz, S. A. Shamma, and B. Babadi, Adaptive Sparse Logistic Regression with Application to Neuronal Plasticity Analysis, 2015 Asilomar Conference on Signals, Systems, and Computers, Nov. 8–11, Pacific Grove, CA (invited).

S. Akram, J. Z. Simon, B. Babadi, Dynamic Estimation of Auditory Temporal Response Function from MEG with Confidence Intervals, Proceedings of the 45th Annual Neuroscience Meeting (SfN 2015), Oct. 17—21, Chicago, IL.

A. Sheikhattar, J. B. Fritz, S. A. Shamma, and B. Babadi, Adaptive Estimation of Sparse Point Process Models Enhances Resolution of Spectrotemporal Receptive Field Plasticity Analysis, Proceedings of the 45th Annual Neuroscience Meeting (SfN 2015), Oct. 17—21, Chicago, IL.

2014

D. Ba, B. Babadi, P. L. Purdon, and E. N. Brown, Robust Spectrotemporal Decomposition by Iteratively Re-weighted Least Squares, Proceedings of the National Academy of Sciences, Vol. 111, No. 50, E5336–E5345, Dec. 2014.

B. Babadi and E. N. Brown, A Review of Multitaper Spectral Analysis, IEEE Trans. on Biomedical Engineering, Vol. 61, No. 5, pp. 1555-1564, May 2014.

E A. Mukamel, E. Pirondini, B. Babadi, K. F. K. Wong, E. T. Pierce, P. Grace Harrell, J. L. Walsh, A. F. Salazar-Gomez, S. S. Cash, E. N. Eskandar, V. S. Weiner, E. N. Brown, and P. L. Purdon, A Transition in Brain State During Propofol-Induced Unconsciousness, Journal of Neuroscience, Vol. 34, No. 3, pp. 839-845, Feb. 2014.

B. Babadi†, G. Obregon-Henao†, C. Lamus, M. S. Hämäläinen, E. N. Brown, and P. L. Purdon, A Subspace Pursuit-based Iterative Greedy Hierarchical Solution to the Neuromagnetic Inverse Problem, NeuroImage, Vol. 87, pp. 427-443, Feb. 2014 († denotes co-first authorship).

D. Ba, B. Babadi, P. L. Purdon, and E. N. Brown, Convergence and Stability of Iteratively Re-weighted Least Squares Algorithms, IEEE Trans. on Signal Processing, Vol. 62, No. 1, pp. 183-195, Jan. 2014.

S. Akram, J. Z. Simon, S. A. Shamma, and B. Babadi, A State-Space Model for Decoding Auditory Attentional Modulation from MEG in a Competing-Speaker Environment, 2014 Neural Information Processing Systems (NIPS), Dec. 8–12, 2014, Montréal, QC, Canada.

A. Kazemipour, B. Babadi, and M. Wu, Sparse Estimation of Self-Exciting Point Processes with Application to LGN Neural Modeling, IEEE Global Conference on Signal and Information Processing (GlobalSIP), Dec. 3–5, 2014, Atlanta, GA.